


Something Missing

by Magi_Silverwolf



Series: Some IronAgent Trilogy [2]
Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe
Genre: Bot Feels, Gen, Hacking, Logistics, Lying to a Spy is a Bad Idea, Memory Alteration, Memory Loss, Mentions of suicidal intentions, Nick Fury Lies, Polyamory, Sexually Open Committed Relationship, ironagent - Freeform
Language: English
Status: Completed
Published: 2018-02-13
Updated: 2018-02-13
Packaged: 2019-03-17 15:40:40
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 2,571
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13662054
Author URL: https://archiveofourown.org/users/Magi_Silverwolf/pseuds/Magi_Silverwolf
Summary: Phil woke up knowing that something wasn't the same as it was before he almost died. It should not have taken a hacker for him to find out the truth.





	Something Missing

**Author's Note:**

> **Disclaimer** : I do not own the original canon nor am I making any profit from writing this piece. All works are accredited to their original authors, performers, and producers while this piece is mine. No copyright infringement is intended. I acknowledge that all views and opinions expressed herein are merely my interpretations of the characters and situations found within the original canon and may not reflect the views and opinions of the original author(s), producer(s), and/or other people.  
>  **Warnings** : This story may contain material that is not suitable for all audiences and may offend some readers. Specifically, suicidal actions are referenced. Please utilize understanding of personal sensitivities before and while reading.  
>  **Author’s Note** : That romance challenge has rare ships as an acceptable entry. So I’m using it as an excuse to create sad IronAgent content. I got distracted by Iron Jizz, though, so I have a lot of Romance Challenge fills to catch up on. As a reference for the timelines given within the story, my numbers come from a collection of scene stamps given within the comic tie-ins.

-= LP =-  
Something Missing  
-= LP =-  
“If you love, you will grieve, and that’s just a given.” – Kay Redfield Jamison  
-= LP =-

 

Phil Coulson knew that something was missing.

 

Like a phantom limb, it haunted him since the moment he woke up. His memories held strange patches of blurriness as if something was only half-remembered, as if someone had tried to erase something, to _suppress it_ even as it refused to be wiped. That whatever-it-was screamed for acknowledgement and there were moments, far more than he would let anyone know, that Phil wanted to rip even his best friends to pieces for the pain held in those screams.

 

It made no more sense than the moments when Phil would turn to say something to an empty space. It made more sense when Phil realized that he would reach across his bed for _someone_ who wasn’t there.

 

Eight seconds wasn’t long enough to forget whoever was supposed to fill the empty spaces. Phil played around with the time as he shared the story, keeping a careful eye on those around him. Maria and Melinda weren’t nearly as good at blankness as they thought they were. Nick was better at covering up lies with _conviction_ , but that was a tell in itself. Confidence always meant that he was hiding something.

 

Phil was one of the best actual spies that SHIELD had, still field sharp and slowly being convinced that there was something more going on than a near-death. Slowly, too slowly, _far too slowly_ , he noticed the list of conditioned responses beyond the phantom sense of loss. Tropical vacations can be wonderous but calling them magical every single time was a bit much. His fingers shouldn’t twitch at every word that rhymed with ‘ark’. After a certain age, a man deserved to own a nice car, but Phil was not ignorant that he was extremely protective of Lola, as if she was a stand-in for his phantom partner more than a spectacular engineering marvel.

 

Nick shouldn’t have restricted Phil’s access to his own medical records.

 

Or if he had, he should have thought to close other avenues of research.

 

Turns out that knowing a hacker was useful for getting into places where people tried to hide things. Turns out that said hacker was far more loyal to a _person_ than to a governmental shadow organization.

 

Of course, one would imagine that the director of an intelligence organization would _know_ that and would consequently forbid someone who specializes in asset logistics from becoming the handler for a hacker outside said organization. Either Nick was dropping the ball uncharacteristically or the source he planted on the plane hadn’t netted him information of Skye’s adaptability and tenacity yet. Their window for collusion was most likely going to be small so they had better make it fruitful.

 

Skye’s crowing over accessing Lola’s service records from the SHIELD central database lasted a grand total of forty-five seconds before she registered the back-hack. By that point whatever defensive measure was causing the hack had infiltrated the systems of the plane. Skye watched with increasingly visible guilt as the other hacker worked their way through mission and flight logs. The inventory manifests held particular interest, with the detailed lists of Phil’s collection being sorted three times in rapid succession.

 

Phil was already planning his brief when the invader accessed the onboard biological scanner with a speed and precision which he knew should have been intimately familiar. He could feel that in his gut, in the same place that told him that something was missing more than just time. Skye cursed as she tried to shut down the invasion, fingers flying as she futilely tried to put more speed behind her typing.

 

“Agent Coulson,” announced a voice from the nearby intercom speaker. Phil analyzed it quickly as British, male, and tauntingly _familiar_. His heart beat achingly hard beneath his sternum. It was just another thing stolen from him, another memory that he should have but didn’t. God, Nick, what did you do? “Lola has currently missed six diagnostic reviews and Sir has created three different updates for her systems. I am authorized to initiate the updates, if you are still interested in allowing Sir access to her mainframe.”

 

There was something in the tone, something that bothered Phil more than it should. The tone was perfectly neutral, without any apparent anger or judgement. It lacked the warmth that should have been present. His head ached from the need to remember why he expected affection from a stranger. The emptiness that he had been chasing for _months_ surged inside him, screaming once more for recognition and chafing at its restraints. Luckily, Skye decided to guide the conversation.

 

“Yeah, um, hi, since you seem to know AC, maybe you could give us a handle in return? And maybe an explanation for how you know the good agent?”

 

“Am I to infer from your questions that Agent Coulson has not divulged his relationship with Sir?”

 

“Uh, see I have a feeling that this will be even weirder than wormholes spewing an alien army and my life is apparently a soap opera as well as a comic book, I’m gonna say Coulson does not even recall his relationship with ‘Sir’. So can you help us out with a few details?”

 

“Of course, Miss,” the voice replied, sounding much warmer. “My designation is JARVIS. I am a constructed intelligence made by Tony Stark. Agent Coulson entered into a relationship with Sir on the twelfth of August, 2006. While not discussed within my hearing, it is my conclusion that the relationship is of a romantic nature with open parameters on sexual congress. In the eighty-two days since Sir was told Agent Coulson had been killed, there have been five instances of behavior matching the parameters set by Agent Coulson as cause for immediate contact, the first being within the confines of the Battle of New York and the most recent one being yesterday’s public challenge to the Mandarin which included the address to Sir’s Malibu residence.”

 

“Let me see if I understand this,” Phil replied. “I had been in a committed relationship for over four years when Loki stabbed me on the Helicarrier. My partner was informed of my death as if it were a permanent thing instead of the mere eight seconds I was told. For whatever reason, I cannot recall this relationship and have not been informed that I had left behind more than a cellist with a crush.”

 

“Don’t forget about being sent to Tahiti,” Skye quipped. She grinned wryly as Phil automatically made his reply.

 

“It’s a magical place.” Phil let the words settle in the air a moment before continuing. “JARVIS, where is Melinda May currently?”

 

“Agent May is currently alone in the main hanger. Before you seek her out, there is another issue of which you should be made aware.” Both Phil and Skye tensed at the AI’s words. Phil took a deep breath that he released slowly. It would do no good to panic without knowing what had happened. “The Malibu residence was fired upon repeatedly yesterday evening, culminating in its plummet into the sea. Sir was present at the time as were Miss Potts and an unauthorized guest. I initiated Protocol Taser to remove him to an undisclosed location and restrict his access to his SI credentials. So far his only attempt at circumventing this restriction was to leave a message for Miss Potts. Though the continued lack of activity on his monetary holdings is concerning, Sir was in moderate health when I last scanned him, allowing for the previous conditions arising from sleep deprivation and mild malnutrition.

 

“There is another matter, however, of growing concern. The crew removing the debris of the mansion is not following my instructions to detour efforts towards the portion at the base of the cliff. I currently do not have access to the resources to retrieve Dummy, U, and Butterfingers. Sir’s precautionary measures against outside tampering prevents me from backing up their coding without Sir’s input. At current rates of degradation, retrieval may become more sentimental than preservative by the time Sir returns.”

 

“Have you integrated yourself enough to redirect the autopilot?”

 

“I have, Agent Coulson. Where would you like me to take you?”

 

“Malibu, if you would,” Phil replied, making Skye take a sharp breath, “and as close to the mansion as possible.”

 

“Oh, May is gonna freak. Do we even know what we’re retrieving?”

 

“Sir’s bots,” JARVIS helpfully supplied. “They are also constructed intelligences.”

 

“Oh, god,” Skye said as the implications hit home. Her eyes were wide and wet as they met his. Phil gave her a sharp nod. As a coding expert, Skye would recognize the subtle differences in the language being used. She would _understand_ so much better than anyone on the plane except Fitz. If he didn’t walk away from SHIELD over this (because he knew that she would follow if he did), she would be ideal for a Welcome Wagon team. He gave her his blandest smile as they felt the plane turning.

 

“Leave Agent May to me. I want you to start the logistics of the rescue with JARVIS.”

 

Phil met her in the common area. She would have headed towards the cockpit the moment the plane had turned. Her wrists were still taped, indicating that she had been working the bag before heading up. Phil glanced at Ward standing behind her and reassessed what she may have been doing. The two specialists were likely sparring.

 

“What’s going on, Coulson?” Melinda asked. Years of working together made her able to read his body language enough to know that they weren’t under attack despite the fact that neither of the official pilots were responsible for the change in direction.

 

“Rescue mission, priority one,” Phil replied. “Skye’s working with our contact on logistics. Fitz will be needed as part of the ground team.”

 

“Simmons is biology,” Ward reminded. Phil gave him a particularly placid smile. He honestly could not understand why people got the two scientists mixed up, despite how long they had functioned as an effective unit. Under normal circumstances, he would only be mildly annoyed by the implication that he did the same. Unfortunately for Ward, Phil was already angry.

 

“Tell Fitz to report to my office? I need to speak with Agent May alone.”

 

“Yes, sir.”

 

Phil and Melinda stared at each other until Ward was definitely gone. Melinda fell into a parade rest, the very picture of relaxed and open. It was only because she was _his_ specialist that Phil could see the undercurrent of tension running through her. He deliberately let the silence stretch for as long as he dared given that Ward and Fitz would have to come through the room to get to his office.

 

“I’m very upset with you. Fury and Hill? I would expect this from them. Fury is perfectly willing to sacrifice _everything_ in the name of security, including his own family, and Hill would do anything Fury ordered her to. It’s why she’s his SiO and not me. But you?” He spat the last word at her. A small vindictive part of him reveled in her tiny flinch. “I’m sure that you _believed_ that you had good reasons for covering up the tampering done to my memories. I’m going to want to hear all of them once this mission is completed in full. I can already tell that I will relish destroying every single one.”

 

“Understood,” Melinda replied. She raised her chin slightly, stubbornly. Her dark eyes were hard. She was accepting of his unspoken limits while disagreeing. That was fine. _For now_. “The mission?”

 

“The Malibu residence of Tony Stark was destroyed late yesterday.” He watched as she startled out of her battle-ready neutrality. He gave a sharp nod before twisting the knife. “Apparently, Stark gave out the address on live television and issued a challenge to a known terrorist who promptly responded. JARVIS was forced to extract Stark for his own safety. This was not the _first time_ he’s done something along these lines since being informed that I had _died_.” Phil forced himself to take a deep breath, trying not to focus on the reasons behind the need for the protocols he had put in place and what their activations would mean. He recognized them too well from managing his problematic assets, the ones whose greatest threat was from themselves. “First, we’re going to recover the bots.”

 

“That explains why Fitz is on the ground team. Then we’ll meet up with Tony?”

 

The phrasing made him reassess how they could have possibly gotten to this point. As the only other senior agent on the team, it would make sense for Melinda to be Fury’s source. Yet the Director had not been fully briefed on Skye’s capabilities. Then Melinda, who habitually defaulted to surnames for even him, had called Tony by name.

 

“You engineered this.”

 

“I allowed it to happen,” she corrected. One corner of her mouth raised as if silently reminding him that there was a difference between the two instances. “Fury had his reasons for creating the situation. I agree with some of them. Personal feelings aside, separating you and Tony has more risk than reward, as you are both better together, which Fury would have seen had he not been blinded by the personality conflict with Tony. To paraphrase his own words, I acknowledge that he made a decision but as it is a foolish decision, I elected to not follow it.”

 

“That does sound like something he would say.”

 

“He said it while countermanding the WSC’s order to nuke New York. When they overrode him, he contacted Tony directly to inform him of the incoming warhead. It hadn’t been a full two hours since he announced your death _over the public comms_ before yanking Tony into a meeting with himself and _Steve Rogers_.” Melinda was visually angry as she spoke. Phil could feel the echo of it within himself as he pictured how it would have played out. An asset that had safety protocols in place in case of suicidal recklessness and had recently suffered the death of a long-term partner should not have been allowed anywhere near that task. Even allowing them into the field was questionable, but sometimes it was necessary.

 

“Don’t hold back, May. Express yourself.”

 

“I hear beating up friends is good stress relief.” She didn’t smile as she said it, but he could tell that she was doing it on the inside. It seemed like it had been too long since he had that impression from her. For the first time since waking up, Phil felt like he knew the direction he needed to head. As if reading his mind, Melinda’s lips curled slightly. “It is good to have you back, Coulson.”

 

“Still missing a few parts.”

 

“I know a decent mechanic. He has a few issues and he’s a bit of an asshole, but he’s a good man.”

 

“Is he?”

 

“One of the best,” Melinda said without hesitation, “and a big damn hero even at his worst.”

 

“You _like_ him.”

 

“He grows on you,” she allowed, “like a fungus.”

 

“Who’s a fungus?”

 

“Our next mission,” Phil answered Fitz, sliding easily into the headspace of team leader. Things would sort themselves out in due time. For now, they had a rescue and reunion to plan.

 

-= LP =-  
An Ending  
-= LP =-

**Author's Note:**

> Challenge Information:  
> Day/Fic: 03  
> Representation(s): Rare Ship (IronAgent)  
> Word Count: 2545 (Story Only); 2562 (Story & Epigraph)


End file.
